Does the user running Apache have rights to the
/home/soumya/Application/BLAST/blastall file and the data directories?
What's in the access_log or error_log when you run the script from the
web page?
-Michael
>>> Soumyadeep nandi <[EMAIL PROTECTED]> 03/25/03 07:39AM >>>
Hi,
I am stuck with another problem. I want to send a
request from the perl file to the server. The server
receives the request with a cgi file which will
process the request by executing a system command and
send back the result. But my cgi script is not
executing the system command.
The cgi script I wrote as file3.cgi as bellow:
#!/usr/bin/perl -w
use CGI;
print "Content-type:text/plain\n\n";
$query = new CGI;
print "blast\n";
$str = $query->param('st');
print "here the string is : $str\n";
system("/home/soumya/Application/BLAST/blastall -p
blastn -d /home/soumya/Application/BLAST/data/ecoli.nt
-i /var/www/cgi-bin/bic_genscan/testseq -o
/var/www/cgi-bin/bic_genscan/testblastout");
-------------------------
This command in the above script is calling another
program(blastall) residing in
/home/soumya/Application/BLAST, and -p,
-d, -i and -o are the arguments required as a
parameter to run the program.
This command should create a file (testblastout) in
the directory(/var/www/cgi-bin/bic_genscan), as I've
passed the name as the argument (-o
/var/www/cgi-bin/bic_genscan/testblastout) in the
command.
But it is not creating any file there. Then I wrote a
perl script so that the job could be done.
The perl script is as perl1.pl as bellow:
#!/usr/bin/perl
$str = shift;
chomp = $str;
print "received the sequence\n";
system("/home/soumya/Application/BLAST/blastall -p
blastn -d /home/soumya/Application/BLAST/data/ecoli.nt
-i /var/www/cgi-bin/bic_genscan/\"$str\" -o
/var/www/cgi-bin/bic_genscan/testblastout");
print "done...\n";
-----------------------------
And replaced the system... line in cgi file with
system("./perl1.pl testseq");
Still it is not executing the system command.
If I run this perl file alone without calling it from
any other file then it executes. (./perl1.pl testseq
from command line).
What should I do to run the system command either from
cgi or perl file in this above scenario.
As I can not see my earliar mail depicting the same
problem in the list I am sending it again. I am sorry
if this mail is showing twice.
With regards,
Soumyadeep
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